GIT microbiome mapping - which is the right test for your health goal?

by Robyn Cogger
5 minutes
GIT microbiome mapping - which is the right test for your health goal?

There are many types of gastro-intestinal tract (GIT) tests available, and each one has advantages and limitations. Understanding these different types of tests may help you choose the right one. 

Faecal occult blood screen

You may of heard your GP talk about stool testing as a screening for colon cancer. In Australia, turning 50 years old, the government sends you a stool test in the mail. This is a faecal occult blood test which is designed to detect blood in the stool, an established biomarker for detecting colon cancer. 

It only tests one biomarker for gut health, the presence of blood in the stool. However, it provides no information about overall gut health.

Three day Parasitology

If you ever had bad belly after travelling to another country, you may of heard of the 3-day parasitology. This test involves taking samples over 3 days and is the most reliable method for identifying protozoa parasites Blastocystis hominis, Dientamoeba fragilis, Giardia lamblia, Endomilax nana, Entamoeba histolytica and Cryptosporidium parvum. These organisms can only be detected when they are shedding and so multiple tests over several days is needed.  This test is the most reliable test if you have a severe acute gut condition following exposure through water supply or travelling abroad. This test only checks for protozoa infections and nothing else.

Comprehensive digestive stool analysis (CDSA)

This test is a decades old traditional method of stool screening for specific pathogens associated with disease. This method involves placing a stool sample on an agar petrie dish to observe what grows in the sample. It’s used to identify specific pathogenic bacteria that are associated with a disease diagnosis, such as salmonella and E.coli infections. For a long time, this has been the extent of the technology in understanding what was in the GIT microbiome.

New technology has revealed it to be an unreliable testing method with a high rate of false positive/negative results. What grew in the petrie dish did not reflect what was in the gut, and only a small select group of oxygen loving bacteria could grow in petrie culture. The majority of microbes thrive in anaerobic environments and do not grow on a culture plate in an open lab. 

Multiplex PCR and 16S sequencing 

This test involves gene sequencing pathogens in a stool sample. Only a few cells need to be present for this test to detect an organism.  So it is much more sensitive than an CDSA and consequently a more accurate and reliable test compared to the CDSA. It is useful for detecting pathogens that are associated with chronic illness such as H. Pylori, even if it's present in small populations. It will detect other non-bacterial organisms such as fungi, worms and viruses. It also can detect protozoa infections, but not as reliably as the 3 day parasitology. 

This test will only detect what the searcher is looking for. So, there is some bias in the results and the test is not a complete picture of what is in there. Most tests on the market will list about 30 genus groups in their search.

The test also only provides genus level, not species level which may be not enough information. For example, Clostridia genus has a large number of beneficial species, with only a small number of pathogenic species. This test will not reliably differentiate between good and bad species.  It also can’t reliably measure the healthiness of a gut and its functional performance. 

This test is ideal if you want to a sensitive reliable scan for all pathogens associated with disease, and you’re not sure where to start or what the problem might be. 

Metagenomic sequencing

This test is a recent technological advance allowing us to peer into the microbiome with ever greater precision and accuracy. It sequences every fragment of the stool sample providing every genus, species within the genus, and their percentage abundance, including the ones you weren’t looking for in CDSA and PCR method. So this is beneficial when you’re trying to pick out Clostridia difficile amongst a large genus group of mostly beneficial Clostridia, or maybe differentiating between beneficial and harmful Streptococcus species. The greatest power of this test is it can depict the overall function of the microbiome as favouring good health and resistance to disease, or contributing to poor health and disease opportunity. 

This test isn’t ideal for detecting infectious organisms larger than bacteria, such as fungi and protozoan parasites. It also doesn’t detect viruses whereas 16S & PCR tests can.

It’s ideal for assessing how the microbiome might contribute to good/poor health and disease susceptibility.

You can read more about the testing I offer here.

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(19)30420-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312819304202%3Fshowall%3Dtrue

Photo of Robyn Cogger from Arising Health


Arrange a consultation today

Australian and international clients via telehealth.

Online bookings now available.

Free 20 min Q&A.